SELVa: Simulator of evolution with landscape variation

Organisms evolve to increase their fitness, a process that may be described as climbing the fitness landscape. However, the fitness landscape of an individual site, i.e., the vector of fitness values corresponding to different variants at this site, can itself change with time due to changes in the environment or substitutions at other epistatically interacting sites. While there exist a number of simulators for modeling different aspects of molecular evolution, very few can accommodate changing landscapes. We present SELVa, the Simulator of Evolution with Landscape Variation, aimed at modeling the substitution process under a changing single-position fitness landscape in a set of evolving lineages that form a phylogeny of arbitrary shape. Written in Java and distributed as an executable jar file, SELVa provides a flexible framework that allows the user to choose from a number of implemented rules governing landscape change.

Estimating Prosopis pod production in the drylands of Magadi in Kajiado, Kenya

Prosopis juliflora was introduced in Baringo County in the Rift valley, Kenya as a shrub species to rehabilitate the denuded dry lands. It became invasive and spread to other pastoralist areas in Kenya, including Magadi region thereby competing and replacing other vegetation types. Past research has however shown that its pods have proven qualities for use as animal feedstuff. This study was undertaken with the objective of establishing whether Prosopis juliflora pods in the drylands of Magadi area in Kajiado County was in sufficient quantities for production of animal feeds. Pods were collected and weighed once a week in randomly selected and fenced 30 x 30-meter plots in the Nguruman escarpment and the Olkiramatian floodplains. Three categories of plots based on plant density were marked out as dense, moderate and sparse respectively. Half of the dense plots had their Prosopis trees pruned and thinned to allow spacing of five meters (managed dense). Weekly collection and weighing of pods was carried out for a period of ten months including one wet season and two dry seasons. The managed dense, unmanaged dense, moderate and sparse plots yielded 44.3 tonnes per hectare (tha-1,) 24.5 tha-1, 15.4 tha-1 and 1.3 tha-1 in Nguruman escarpment and 9.3 tha-1, 17.6 tha-1, 1.5 tha-1 and 0.2 tha-1 in the Olkiramatian floodplains respectively. The management practice of pruning and spacing increased pod yield production in the well-watered escarpment landscape. The lowest and highest pod yields were recorded during the dry season and the rainy season respectively. The results showed that the dense unmanaged plots in the lowland landscapes had higher pod yields when compared to the managed dense plots in the escarpment landscape. Variation in pod yields was analyzed using Genstat 14th edition. The results from this study found that the managed Prosopis stands located in the escarpment

Gradient analysis of landscape variation in Norway

SUMMARYA multitude of landscape characterisation and mapping methods exist, but few methods take into account that landscapes properties vary in a gradual, continuous manner along multiple directions of variation. In this study, we used gradient analytic methods, rooted in ecological continuum theory, to analyse landscape variation throughout Norway. The aim is to explain differences in landscape properties in the simplest possible way, by identifying ‘complex landscape gradients’ (CLGs), i.e. composite gradients of co-occurring landscape elements and properties.We collected data by stratified sampling of 100 test areas (20×20 km), in which we delineated a total of 3966 observation units (landscape polygons 4–30 km²) based on geomorphological criteria. For each observation unit, 85 landscape variables were recorded. We identified patterns of variation in landscape element composition by parallel use of two multivariate statistical methods, detrended correspondence analysis (DCA) and global nonmetric multidimensional scaling (GNMDS).The analyses revealed that the most important properties explaining differences in total landscape elements composition was location of the landscape relative to the coastline and coarse-scale landform variation. Most landscape elements had distinct optima within specific segments along broad-scale complex-gradients in landscape properties. A tentative landscape-type hierarchy was built by an iterative procedure by which the amount of compositional turnover in landscape-element composition between adjacent types was standardised. Six ‘major landscape types’ were identified based on geomorphological criteria. Within each major type, we identified a unique set of 2–5 important CLGs, representing geo-ecological, bio-ecological, and land use-related landscape variation. Minor landscape types were obtained by combining segments along two or more CLGs.The study shows that geological diversity, biological diversity and human land-use are tightly intertwined at the landscape level of ecological complexity, and that predominantly abiotic processes control and constrain both biotic processes and human land use.

Wetland Loss Identification and Evaluation Based on Landscape and Remote Sensing Indices in Xiong’an New Area

Wetlands play a critical role in the environment. With the impacts of climate change and human activities, wetlands have suffered severe droughts and the area declined. For the wetland restoration and management, it is necessary to conduct a comprehensive analysis of wetland loss. In this study, the Xiong’an New Area was selected as the study area. For this site, we built a new method to identify the patterns of wetland loss integrated the landscape variation and wetland elements loss based on seven land use maps and Landsat series images from the 1980s to 2015. The calculated results revealed the following: (1) From the 1980s to 2015, wetland area decreased by 40.94 km2, with a reduction of 13.84%. The wetland loss was divided into three sub stages: the wet stage from 1980s to 2000, the reduction stage from 2000 to 2019 and the recovering stage from 2009 to 2015. The wetland area was mainly replaced by cropland and built-up land, accounting for 98.22% in the overall loss. The maximum wetland area was 369.43 km2 in the Xiong’an New Area. (2) From 1989 to 2015, the normalized difference vegetation index (NDVI), normalized difference water index (NDWI) and soil moisture monitoring index (SMMI) showed a degradation, a slight improvement and degradation trend, respectively. The significantly degraded areas were 80.40 km2, 20.71 km2 and 80.05 km2 by the detection of the remote sensing indices, respectively. The wetland loss was mainly dominated by different elements in different periods. The water area (NDWI), soil moisture (SMMI) and vegetation (NDVI) caused the wetland loss in the three sub-periods (1980s–2000, 2000–2009 and 2009–2015). (3) According to the analysis in the landscape and elements, the wetland loss was summarized with three patterns. In the pattern 1, as water became scarce, the plants changed from aquatic to terrestrial species in sub-region G, which caused the wetland vegetation loss. In the pattern 2, due to the water area decrease in sub-regions B, C, D and E, the soil moisture decreased and then the aquatic plants grew up, which caused the wetland loss. In the pattern 3, in sub-region A, due to the reduction in water, terrestrial plants covered the region. The three patterns indicated the wetland loss process in the sub region scale. (4) The research integrated the landscape variation and element loss appears potential in the identification of the loss of wetland areas.

Transcriptome Landscape Variation in the Genus Thymus

Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.

SELVa: Simulator of Evolution with Landscape Variation

Organisms evolve to increase their fitness, a process that may be described as climbing the fitness landscape. However, the fitness landscape of an individual site, i.e., the vector of fitness values corresponding to different variants at this site, can change with time due to changes in the environment or substitutions at other epistatically interacting sites. We present SELVa, the Simulator of Evolution with Landscape Variation, aimed at modeling the substitution process under a changing single position fitness landscape in a set of evolving lineages forming a phylogeny of arbitrary shape. Written in Java and distributed as an executable jar file, SELVa provides a flexible framework that allows the user to choose from a number of implemented rules governing landscape change.Availabilityhttps://github.com/bazykinlab/SELVa